[maker-devel] Inconsistent RepeatMasker error on draft assembly

[Carson Holt]

If running under MPI, you can get messages from multiple processes (slightly out of order), in which case the more descript cause of the error may be further upstream in the STDERR log. If running without MPI, and the error you see is matched with the Widget::RepeatMasker command used, then you can simply copy it and run it outside of MAKER. If there are installation issues with your RepeatMasker copy then the cause will become more apparent.

i.e. Run the command by itself —> /scratch/exe/RepeatMasker/RepeatMasker /scratch/bin/or_test3.maker.output/or_test3_datastore/E3/2F/scaffold2852_size18614//theVoid.scaffold2852_size18614/0/scaffold2852_size18614.0.all.rb -species all -dir /scratch/bin/or_test3.maker.output/or_test3_datastore/E3/2F/scaffold2852_size18614//theVoid.scaffold2852_size18614/0 -pa 2

—Carson


> On Aug 11, 2017, at 12:43 PM, Zach Cohen <zachary.pcohen at gmail.com> wrote:
> 
> Hello All,
> I'm receiving a RepeatMasker on some (not all) of my scaffolds. 
> Widget::RepeatMasker:
> 
> cd /tmp/maker_7hGhhm; /scratch/exe/RepeatMasker/RepeatMasker /scratch/bin/or_test3.maker.output/or_test3_datastore/E3/2F/scaffold2852_size18614//theVoid.scaffold2852_size18614/0/scaffold2852_size18614.0.all.rb -species all -dir /scratch/bin/or_test3.maker.output/or_test3_datastore/E3/2F/scaffold2852_size18614//theVoid.scaffold2852_size18614/0 -pa 2
> 
> #-------------------------------#
> 
> ERROR: RepeatMasker failed
> 
> --> rank=NA, hostname=82853d8df2a5
> 
> ERROR: Failed while doing repeat masking
> 
> ERROR: Chunk failed at level:0, tier_type:1
> 
> FAILED CONTIG:scaffold2852_size18614
> 
> ERROR: Chunk failed at level:2, tier_type:0
> 
> FAILED CONTIG:scaffold2852_size18614
> 
> examining contents of the fasta file and run log
> 
> 
> 
> I'm not sure if there is an issue with the widget itself, as this doesn't come up for all the scaffolds and the example data seemed to run fine, or a problem with these particular scaffolds. Thanks for any assistance you can provide!
> 
> Best,
> 
> Z
> 
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